Performs fastq alignment to a fasta reference using using gem3-mapper
meta:map
Groovy Map containing reference/index information e.g. [ id:‘test’ ]
gem:file
GEM3 genome index files
*.{gem}
meta2:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
fastq:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
*.{fastq,fq,fastq.gz,fq.gz}
sort_bam:boolean
use samtools sort (true) or samtools view (false)
true or false
bam
*.bam:file
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
versions
versions.yml:file
File containing software versions
versions.yml
The GEM indexer (v3).
